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Ammarah U, Pereira-Nunes A, Delfini M, Mazzone M. From monocyte-derived macrophages to resident macrophages-how metabolism leads their way in cancer. Mol Oncol 2024; 18:1739-1758. [PMID: 38411356 DOI: 10.1002/1878-0261.13618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Macrophages are innate immune cells that play key roles during both homeostasis and disease. Depending on the microenvironmental cues sensed in different tissues, macrophages are known to acquire specific phenotypes and exhibit unique features that, ultimately, orchestrate tissue homeostasis, defense, and repair. Within the tumor microenvironment, macrophages are referred to as tumor-associated macrophages (TAMs) and constitute a heterogeneous population. Like their tissue resident counterpart, TAMs are plastic and can switch function and phenotype according to the niche-derived stimuli sensed. While changes in TAM phenotype are known to be accompanied by adaptive alterations in their cell metabolism, it is reported that metabolic reprogramming of macrophages can dictate their activation state and function. In line with these observations, recent research efforts have been focused on defining the metabolic traits of TAM subsets in different tumor malignancies and understanding their role in cancer progression and metastasis formation. This knowledge will pave the way to novel therapeutic strategies tailored to cancer subtype-specific metabolic landscapes. This review outlines the metabolic characteristics of distinct TAM subsets and their implications in tumorigenesis across multiple cancer types.
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Affiliation(s)
- Ummi Ammarah
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, Belgium
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Italy
| | - Andreia Pereira-Nunes
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, Belgium
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Marcello Delfini
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, Belgium
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Shasha C, Glass DR, Moelhman E, Islas L, Tian Y, Szeto GL, Peng T, Song X, Wurscher M, Bumol TF, Torgerson TR, Greenberg PD, Green DJ, Newell EW. Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597178. [PMID: 38895348 PMCID: PMC11185627 DOI: 10.1101/2024.06.03.597178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the induction of exhaustion in tumor-specific T cells. However, the extent of T cell tumor recognition and exhaustion is not well-characterized in MM. As the specific mechanisms of immune evasion are critical for devising effective therapeutic strategies, we deeply profiled the CD8+ T cell compartment of newly-diagnosed MM (NDMM) patients for evidence of tumor reactivity and T cell exhaustion. We applied single-cell multi-omic sequencing and antigen-specific mass cytometry to longitudinal BM and peripheral blood (PB) samples taken from timepoints spanning from diagnosis through induction therapy, autologous stem cell transplant (ASCT), and maintenance therapy. We identified an exhausted-like population that lacked several canonical exhaustion markers, was not significantly enriched in NDMM patients, and consisted of small, nonpersistent clones. We also observed an activated population with increased frequency in the PB of NDMM patients exhibiting phenotypic and clonal features consistent with homeostatic, antigen-nonspecific activation. However, there was no evidence of "tumor-experienced" T cells displaying hallmarks of terminal exhaustion and/or tumor-specific activation/expansion in NDMM patients at any timepoint.
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Affiliation(s)
- Carolyn Shasha
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David R. Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ernest Moelhman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yuan Tian
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tao Peng
- Allen Institute for Immunology, Seattle, WA, USA
| | - Xiaoling Song
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michelle Wurscher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | - Philip D. Greenberg
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Immunology, University of Washington, Seattle, WA, USA
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan W. Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Sinha S, Vegesna R, Mukherjee S, Kammula AV, Dhruba SR, Wu W, Kerr DL, Nair NU, Jones MG, Yosef N, Stroganov OV, Grishagin I, Aldape KD, Blakely CM, Jiang P, Thomas CJ, Benes CH, Bivona TG, Schäffer AA, Ruppin E. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. NATURE CANCER 2024; 5:938-952. [PMID: 38637658 DOI: 10.1038/s43018-024-00756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024]
Abstract
Tailoring optimal treatment for individual cancer patients remains a significant challenge. To address this issue, we developed PERCEPTION (PERsonalized Single-Cell Expression-Based Planning for Treatments In ONcology), a precision oncology computational pipeline. Our approach uses publicly available matched bulk and single-cell (sc) expression profiles from large-scale cell-line drug screens. These profiles help build treatment response models based on patients' sc-tumor transcriptomics. PERCEPTION demonstrates success in predicting responses to targeted therapies in cultured and patient-tumor-derived primary cells, as well as in two clinical trials for multiple myeloma and breast cancer. It also captures the resistance development in patients with lung cancer treated with tyrosine kinase inhibitors. PERCEPTION outperforms published state-of-the-art sc-based and bulk-based predictors in all clinical cohorts. PERCEPTION is accessible at https://github.com/ruppinlab/PERCEPTION . Our work, showcasing patient stratification using sc-expression profiles of their tumors, will encourage the adoption of sc-omics profiling in clinical settings, enhancing precision oncology tools based on sc-omics.
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Affiliation(s)
- Sanju Sinha
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
| | - Rahulsimham Vegesna
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Sumit Mukherjee
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Ashwin V Kammula
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
- University of Maryland, College Park, MD, USA
| | | | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Matthew G Jones
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute, Cambridge, MA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | | | - Ivan Grishagin
- Rancho BioSciences, San Diego, CA, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Peng Jiang
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA, USA
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, USA.
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Wang L, Wei Y, Jin Z, Liu F, Li X, Zhang X, Bai X, Jia Q, Zhu B, Chu Q. IFN-α/β/IFN-γ/IL-15 pathways identify GBP1-expressing tumors with an immune-responsive phenotype. Clin Exp Med 2024; 24:102. [PMID: 38758367 PMCID: PMC11101573 DOI: 10.1007/s10238-024-01328-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/09/2024] [Indexed: 05/18/2024]
Abstract
Immunotherapy is widely used in cancer treatment; however, only a subset of patients responds well to it. Significant efforts have been made to identify patients who will benefit from immunotherapy. Successful anti-tumor immunity depends on an intact cancer-immunity cycle, especially long-lasting CD8+ T-cell responses. Interferon (IFN)-α/β/IFN-γ/interleukin (IL)-15 pathways have been reported to be involved in the development of CD8+ T cells. And these pathways may predict responses to immunotherapy. Herein, we aimed to analyze multiple public databases to investigate whether IFN-α/β/IFN-γ/IL-15 pathways could be used to predict the response to immunotherapy. Results showed that IFN-α/β/IFN-γ/IL-15 pathways could efficiently predict immunotherapy response, and guanylate-binding protein 1 (GBP1) could represent the IFN-α/β/IFN-γ/IL-15 pathways. In public and private cohorts, we further demonstrated that GBP1 could efficiently predict the response to immunotherapy. Functionally, GBP1 was mainly expressed in macrophages and strongly correlated with chemokines involved in T-cell migration. Therefore, our study comprehensively investigated the potential role of GBP1 in immunotherapy, which could serve as a novel biomarker for immunotherapy and a target for drug development.
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Affiliation(s)
- Lei Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Yuxuan Wei
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Zheng Jin
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400032, People's Republic of China
- Research Institute, GloriousMed Clinical Laboratory (Shanghai) Co., Ltd, Shanghai, 201318, People's Republic of China
| | - Fangfang Liu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Xuchang Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Xiao Zhang
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Army Medical University, Shigatse, 857000, People's Republic of China
| | - Xiumei Bai
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Army Medical University, Shigatse, 857000, People's Republic of China
| | - Qingzhu Jia
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
- Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, People's Republic of China
| | - Bo Zhu
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
- Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, People's Republic of China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China.
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Sun J, Guo H, Nie Y, Zhou S, Zeng Y, Sun Y. Deciphering the heterogeneity dominated by tumor-associated macrophages for survival prognostication and prediction of immunotherapy response in lung adenocarcinoma. Sci Rep 2024; 14:9276. [PMID: 38653742 DOI: 10.1038/s41598-024-60132-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are a specific subset of macrophages that reside inside the tumor microenvironment. The dynamic interplay between TAMs and tumor cells plays a crucial role in the treatment response and prognosis of lung adenocarcinoma (LUAD). The study aimed to examine the association between TAMs and LUAD to advance the development of targeted strategies and immunotherapeutic approaches for treating this type of lung cancer. The study employed single-cell mRNA sequencing data to characterize the immune cell composition of LUAD and delineate distinct subpopulations of TAMs. The "BayesPrism" and "Seurat" R packages were employed to examine the association between these subgroups and immunotherapy and clinical features to identify novel immunotherapy biomarkers. Furthermore, a predictive signature was generated to forecast patient prognosis by examining the gene expression profile of immunotherapy-associated TAMs subsets and using 104 machine-learning techniques. A comprehensive investigation has shown the existence of a hitherto unidentified subgroup of TAMs known as RGS1 + TAMs, which has been found to have a strong correlation with the efficacy of immunotherapy and the occurrence of tumor metastasis in LUAD patients. CD83 was identified CD83 as a distinct biomarker for the expression of RGS1 + TAMs, showcasing its potential utility as an indicator for immunotherapeutic interventions. Furthermore, the prognostic capacity of the RTMscore signature, encompassing three specific mRNA (NR4A2, MMP14, and NPC2), demonstrated enhanced robustness when contrasted against the comprehensive collection of 104 features outlined in the published study. CD83 has potential as an immunotherapeutic biomarker. Meanwhile, The RTMscore signature established in the present study might be beneficial for survival prognostication.
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Affiliation(s)
- Jiazheng Sun
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehua Guo
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yalan Nie
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sirui Zhou
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yalu Sun
- Affiliated Hospital of Jining Medical University, Jining, China.
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Song X, Wei J, Li Y, Zhu W, Cai Z, Li K, Wei J, Lu J, Pan W, Li M. An integrative pan-cancer analysis of the molecular characteristics of dietary restriction in tumour microenvironment. EBioMedicine 2024; 102:105078. [PMID: 38507875 PMCID: PMC10965464 DOI: 10.1016/j.ebiom.2024.105078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Dietary restriction (DR), a general term for dieting, has been demonstrated as an effective intervention in reducing the occurrence of cancers. Molecular activities associated with DR are crucial in mediating its anti-cancer effects, yet a comprehensive exploration of the landscape of these activities at the pan-cancer level is still lacking. METHODS We proposed a computational approach for quantifying DR-related molecular activities and delineating the landscape of these activities across 33 cancer types and 30 normal tissues within 27,320 samples. We thoroughly examined the associations between DR-related molecular activities and various factors, including the tumour microenvironment, immunological phenotypes, genomic features, and clinical prognosis. Meanwhile, we identified two DR genes that show potential as prognostic predictors in hepatocellular carcinoma and verified them by immunohistochemical assays in 90 patients. FINDINGS We found that DR-related molecular activities showed a close association with tumour immunity and hold potential for predicting immunotherapy responses in various cancers. Importantly, a higher level of DR-related molecular activities is associated with improved overall survival and cancer-specific survival. FZD1 and G6PD are two DR genes that serve as biomarkers for predicting the prognosis of patients with hepatocellular carcinoma. INTERPRETATION This study presents a robust link between DR-related molecular activities and tumour immunity across multiple cancer types. Our research could open the path for further investigation of DR-related molecular processes in cancer treatment. FUNDING National Natural Science Foundation of China (Grant No. 82000628) and the Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine Foundation of Guangdong Province (Grant No. 2023LSYS001).
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Affiliation(s)
- Xiaoyi Song
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jiaxing Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wen Zhu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhiyuan Cai
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Kunwei Li
- Department of Radiology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jingyue Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jieyu Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wanping Pan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Man Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Biobank, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Department of Information Technology and Data Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China.
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Wang Z, Kirkwood KL, Wang Y, Du W, Lin S, Zhou W, Yan C, Gao J, Li Z, Sun C, Liu F. Analysis of the effect of CCR7 on the microenvironment of mouse oral squamous cell carcinoma by single-cell RNA sequencing technology. J Exp Clin Cancer Res 2024; 43:94. [PMID: 38539232 PMCID: PMC10976828 DOI: 10.1186/s13046-024-03013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Studies have shown that CCR7, an important inflammatory factor, can promote the proliferation and metastasis of oral squamous cell carcinoma (OSCC), but its role in the tumor microenvironment (TME) remains unclear. This paper explores the role of CCR7 in the TME of OSCC. METHODS In this work, we constructed CCR7 gene knockout mice and OSCC mouse models. Single-cell RNA sequencing (scRNA-seq) and bioinformatics were used to analyze the differences in the OSCC microenvironment between three CCR7 gene knockout mice (KO) and three wild-type mice (WT). Immunohistochemistry, immunofluorescence staining, and flow cytometry were used to analyze the expression of key genes in significantly different cell types between the KO and WT groups. An in vitro experiment was used to verify the effect of CCR7 on M2 macrophage polarization. RESULTS In the mouse OSCC models, the tumor growth rate in the KO group was significantly lower than that in the WT group. Eight main cell types (including tumor cells, fibroblasts, macrophages, granulocytes, T cells, endothelial cells, monocytes, and B cells) were identified by Seurat analysis. The scRNA-seq results showed that the proportion of tumor cells was lower, but the proportion of inflammatory cells was significantly higher in the KO group than in the WT group. CellPhoneDB analysis results indicated a strong interaction relationship between tumor cells and macrophages, T cells, fibroblasts, and endothelial cells. Functional enrichment results indicated that the expression level of the Dusp1 gene in the KO group was generally higher than that in the WT group in various cell types. Macrophage subclustering results indicated that the proportion of M2 macrophages in the KO group was lower than that in the WT group. In vitro experimental results showed that CCR7 can promote M2 macrophage polarization, thus promoting the proliferation, invasion and migration of OSCC cells. CONCLUSIONS CCR7 gene knockout can significantly inhibit the growth of mouse oral squamous cell carcinoma by promoting the polarization of M2 macrophages.
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Affiliation(s)
- Zengxu Wang
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Keith L Kirkwood
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, NY, Buffalo, 14214-8006, USA
| | - Yao Wang
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Weidong Du
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Shanfeng Lin
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Wanhang Zhou
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Cong Yan
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Jiaxing Gao
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Zhenning Li
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Changfu Sun
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China
| | - Fayu Liu
- Department of Oral Maxillofacial-Head and Neck Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, 117 Nanjing North Road, Heping District, Shenyang, Liaoning, 110002, People's Republic of China.
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8
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Qu C, Cui H, Xiao S, Dong L, Lu Q, Zhang L, Wang P, Xin M, Zhi H, Liu C, Ning S, Gao Y. The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses. Commun Biol 2024; 7:327. [PMID: 38485995 PMCID: PMC10940638 DOI: 10.1038/s42003-024-06004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) by cooperating with immunity genes in tumor immunization. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here we present an integrated framework that leverages network-based analyses and Bayesian network inference to identify the regulated relationships including lncRNA, ICP and immunity genes as ICP-related LncRNAs mediated Core Regulatory Circuitry Triplets (ICP-LncCRCTs) that can make robust predictions. Hub ICP-related lncRNAs such as MIR155HG and ADAMTS9-AS2 were highlighted to play central roles in immune regulation. Specific ICP-related lncRNAs could distinguish cancer subtypes. Moreover, the ICP-related lncRNAs are likely to significantly correlated with immune cell infiltration, MHC, CYT. Some ICP-LncCRCTs such as CXCL10-MIR155HG-ICOS could better predict one-, three- and five-year prognosis compared to single molecule in melanoma. We also validated that some ICP-LncCRCTs could effectively predict ICI-response using three kinds of machine learning algorithms follow five independent datasets. Specially, combining ICP-LncCRCTs with the tumor mutation burden (TMB) improves the prediction of ICI-treated melanoma patients. Altogether, this study will improve our grasp of lncRNA functions and accelerating discovery of lncRNA-based biomarkers in ICI treatment.
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Affiliation(s)
- Changfan Qu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hao Cui
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Song Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Longlong Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qianyi Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lei Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mengyu Xin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chenyu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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9
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Mukherjee N, Katsnelson E, Brunetti TM, Michel K, Couts KL, Lambert KA, Robinson WA, McCarter MD, Norris DA, Tobin RP, Shellman YG. MCL1 inhibition targets Myeloid Derived Suppressors Cells, promotes antitumor immunity and enhances the efficacy of immune checkpoint blockade. Cell Death Dis 2024; 15:198. [PMID: 38459020 PMCID: PMC10923779 DOI: 10.1038/s41419-024-06524-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 03/10/2024]
Abstract
Immune checkpoint inhibitors (ICIs) are now the first-line treatment for patients with advanced melanoma. Despite promising clinical results, many patients fail to respond to these therapies. BH3 mimetics, a novel class of small molecule inhibitors that bind and inhibit anti-apoptotic members of the BCL2 family proteins such as BCL2 or MCL1, have been very successful in treating hematologic malignancies. However, there are limited studies on the immunomodulatory role of the BH3 mimetics. Several factors contribute to ICI resistance including myeloid-derived suppressor cells (MDSCs) that exert immunosuppressive effects through direct and indirect inhibition of antitumor immunity. Thus, targeting MDSCs to enhance antitumor immunity has the potential to enhance the efficacy of ICIs. In this study, we show that the MCL1 inhibitor S64315 reduces melanoma tumor growth in an immune cell-dependent manner in mice. Specifically, S64315 enhances antitumor immunity by reducing MDSC frequency and by promoting the activity of CD8+T cells. Additionally, human MDSCs are 10 times more sensitive to S64315 than cutaneous melanoma lines. Further, we found that a higher expression of MCL1 is associated with poor survival for patients treated with anti-PD-1. Finally, combining S64315 and anti-PD-1 significantly slowed tumor growth compared to either agent alone. Together, this proof-of-concept study demonstrates the potential of combining an MCL1 inhibitor with anti-PD-1 in the treatment of melanoma. It justifies the further development of next generation MCL1 inhibitors to improve efficacy of ICIs in treating malignant melanoma.
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Affiliation(s)
- Nabanita Mukherjee
- University of Colorado Anschutz Medical Campus, School of Medicine, Department of Dermatology, Aurora, CO, 80045, USA
| | - Elizabeth Katsnelson
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Surgical Oncology, Aurora, CO, 80045, USA
| | - Tonya M Brunetti
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kylie Michel
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Medical Oncology, Aurora, CO, 80045, USA
| | - Kasey L Couts
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Medical Oncology, Aurora, CO, 80045, USA
| | - Karoline A Lambert
- University of Colorado Anschutz Medical Campus, School of Medicine, Department of Dermatology, Aurora, CO, 80045, USA
| | - William A Robinson
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Medical Oncology, Aurora, CO, 80045, USA
| | - Martin D McCarter
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Surgical Oncology, Aurora, CO, 80045, USA
| | - David A Norris
- University of Colorado Anschutz Medical Campus, School of Medicine, Department of Dermatology, Aurora, CO, 80045, USA
- Department of Veterans Affairs Medical Center, Dermatology Section, Denver, CO, 80220, USA
| | - Richard P Tobin
- University of Colorado Anschutz Medical Campus, School of Medicine, Division of Surgical Oncology, Aurora, CO, 80045, USA.
| | - Yiqun G Shellman
- University of Colorado Anschutz Medical Campus, School of Medicine, Department of Dermatology, Aurora, CO, 80045, USA.
- University of Colorado Anschutz Medical Campus, Gates Center for Regenerative Medicine, Aurora, CO, 80045, USA.
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10
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Xie J, Deng X, Xie Y, Zhu H, Liu P, Deng W, Ning L, Tang Y, Sun Y, Tang H, Cai M, Xie X, Zou Y. Multi-omics analysis of disulfidptosis regulators and therapeutic potential reveals glycogen synthase 1 as a disulfidptosis triggering target for triple-negative breast cancer. MedComm (Beijing) 2024; 5:e502. [PMID: 38420162 PMCID: PMC10901283 DOI: 10.1002/mco2.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Disruption of disulfide homeostasis during biological processes can have fatal consequences. Excess disulfides induce cell death in a novel manner, termed as "disulfidptosis." However, the specific mechanism of disulfidptosis has not yet been elucidated. To determine the cancer types sensitive to disulfidptosis and outline the corresponding treatment strategies, we firstly investigated the crucial functions of disulfidptosis regulators pan-cancer at multi-omics levels. We found that different tumor types expressed dysregulated levels of disulfidptosis regulators, most of which had an impact on tumor prognosis. Moreover, we calculated the disulfidptosis activity score in tumors and validated it using multiple independent datasets. Additionally, we found that disulfidptosis activity was correlated with classic biological processes and pathways in various cancers. Disulfidptosis activity was also associated with tumor immune characteristics and could predict immunotherapy outcomes. Notably, the disulfidptosis regulator, glycogen synthase 1 (GYS1), was identified as a promising target for triple-negative breast cancer and validated via in vitro and in vivo experiments. In conclusion, our study elucidated the complex molecular phenotypes and clinicopathological correlations of disulfidptosis regulators in tumors, laying a solid foundation for the development of disulfidptosis-targeting strategies for cancer treatment.
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Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Xinpei Deng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yi Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Hongbo Zhu
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
| | - Peng Liu
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Wei Deng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Li Ning
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yuhui Tang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yuying Sun
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Hailin Tang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Manbo Cai
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
| | - Xiaoming Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yutian Zou
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
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11
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Yang S, Wang M, Hua Y, Li J, Zheng H, Cui M, Huang N, Liu Q, Liao Q. Advanced insights on tumor-associated macrophages revealed by single-cell RNA sequencing: The intratumor heterogeneity, functional phenotypes, and cellular interactions. Cancer Lett 2024; 584:216610. [PMID: 38244910 DOI: 10.1016/j.canlet.2024.216610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/28/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is an emerging technology used for cellular transcriptome analysis. The application of scRNA-seq has led to profoundly advanced oncology research, continuously optimizing novel therapeutic strategies. Intratumor heterogeneity extensively consists of all tumor components, contributing to different tumor behaviors and treatment responses. Tumor-associated macrophages (TAMs), the core immune cells linking innate and adaptive immunity, play significant roles in tumor progression and resistance to therapies. Moreover, dynamic changes occur in TAM phenotypes and functions subject to the regulation of the tumor microenvironment. The heterogeneity of TAMs corresponding to the state of the tumor microenvironment has been comprehensively recognized using scRNA-seq. Herein, we reviewed recent research and summarized variations in TAM phenotypes and functions from a developmental perspective to better understand the significance of TAMs in the tumor microenvironment.
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Affiliation(s)
- Sen Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Mengyi Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Yuze Hua
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Jiayi Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Huaijin Zheng
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Ming Cui
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Nan Huang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China
| | - Qiaofei Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China.
| | - Quan Liao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, and Peking Union Medical College, Beijing, 100730, China.
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12
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He S, Lu M, Zhang L, Wang Z. RSK4 promotes the macrophage recruitment and M2 polarization in esophageal squamous cell carcinoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166996. [PMID: 38142759 DOI: 10.1016/j.bbadis.2023.166996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
High infiltration of tumor-associated macrophages (TAMs) participates in host immunity and tumor progression in patients with esophageal squamous cell carcinoma (ESCC). Ribosomal s6 kinase 4 (RSK4) has been shown to be aberrantly overexpressed in ESCC. The role of RSK4 in cytokine secretion and its impact on macrophage recruitment and M2 polarization remains unclear. Therefore, a thorough understanding of RSK4 is needed to expand our knowledge of its therapeutic potential. Herein, RSK4 expression in human ESCC tissues and a xenograft mouse model was positively correlated with high infiltration of M0 and M2 macrophages which is positively associated with unfavorable overall survival outcomes and treatment resistance in patients with ESCC. In vitro experiments revealed that RSK4 derived from ESCC cells promoted macrophage recruitment and M2 polarization by enhancingsoluble intercellular adhesion molecule-1 (sICAM-1) secretion via direct and indirect STAT3 phosphorylation. Furthermore, RSK4-induced macrophages enhanced tumor proliferation, migration, and invasion by secreting C-C motif chemokine ligand 22 (CCL22). We further showed that patients with elevated CD68 and CD206 expression had unfavorable overall survival. Collectively, these results demonstrate that RSK4 promotes the macrophage recruitment and M2 polarization by regulating the STAT3/ICAM-1 axis in ESCC, influencing tumor progression primarily in a CCL22-dependent manner. These data also offer valuable insights for developing novel agents for the treatment of ESCC.
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Affiliation(s)
- Shuai He
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China; Department of Pathology, Baotou Medical college, Baotou, Inner Mongolia Autonomous Region, China
| | - Ming Lu
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Pathology, The First Affiliated Hospital of University of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhe Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, China.
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13
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Leroy V, Manual Kollareth DJ, Tu Z, Valisno JAC, Woolet-Stockton M, Saha B, Emtiazjoo AM, Rackauskas M, Moldawer LL, Efron PA, Cai G, Atkinson C, Upchurch GR, Sharma AK. MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576261. [PMID: 38328174 PMCID: PMC10849528 DOI: 10.1101/2024.01.18.576261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Rationale Patients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes. Objectives We examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI. Methods Single-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT), cebpb -/- (MDSC-deficient), Mertk -/- or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice. Measurements and Main Results A significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent in cebpb -/- Land Mertk -/- mice. Adoptive transfer of M-MDSCs in cebpb -/- mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients. In vitro studies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner. Conclusions Our results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.
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14
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Fan Z, Liu Y, Li C, Jiang Y, Wang N, Wang M, Li C, Diao Y, Qiu W, Zhu X, Wang G, Cai S, Yang T, Lv G. T proliferating cells derived autophagy signature associated with prognosis and immunotherapy resistance in a pan-cancer analysis. iScience 2024; 27:108701. [PMID: 38222108 PMCID: PMC10784705 DOI: 10.1016/j.isci.2023.108701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024] Open
Abstract
Despite autophagy modulating tumor immunity in the tumor microenvironment (TME), the immunotherapeutic efficacy and potential mechanism of autophagy signature was not explicit. We manually curated an autophagy gene set and defined a pan-cancer autophagy signature by comparing malignant tissues and normal tissues in The Cancer Genome Atlas (TCGA) cohort. The pan-cancer autophagy signature was derived from T proliferating cells as demonstrated in multiple single-cell RNA sequencing (scRNA-seq) datasets. The pan-cancer autophagy signature could influence the cell-cell interactions in the TME and predict the responsiveness of immune checkpoint inhibitors (ICIs) in the metastatic renal cell carcinoma, non-small cell lung cancer, bladder cancer, and melanoma cohorts. Metabolism inactivation accompanied with dysregulation of autophagy was investigated with transcriptomic and proteomic data. The immunotherapeutic predictive role and mechanism regulation of the autophagy signature was validated in an in-house cohort. Our study provides valuable insights into the mechanisms of ICI resistance.
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Affiliation(s)
- Zhongqi Fan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Yutao Liu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Centre, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Nanya Wang
- Phase I Clinical Trial Unit, First Hospital of Jilin University, Jilin, China
| | - Mingda Wang
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Chao Li
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Yongkang Diao
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Wei Qiu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Xin Zhu
- Burning Rock Biotech, Guangdong, China
| | | | | | - Tian Yang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
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15
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Zhang M, Liang Y, Song P. Identification of prognostic value of anoikis-related gene score model combined with tumor microenvironment score models in esophageal squamous cell carcinoma. J Gene Med 2024; 26:e3624. [PMID: 38087999 DOI: 10.1002/jgm.3624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/21/2023] [Accepted: 10/16/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) has poor survival. Effective prognostic models with high application value remain lack. METHODS Bulk RNA seq and single cell RNA-seq data were retrieved from the XENA-TCGA-ESCC cohort and GSE188900. The anoikis-related gene score (ANO score) model and tumor microenvironment score (TME score) model were constructed and merged into three subgroups. Functional annotation was analyzed by Gene Ontology terms. Univariate and multivariate Cox regression analysis, least absolute shrinkage and selection operator regression analysis and weighted gene coexpression network analysis were performed to construct prognostic prediction models and identify prognostic value. Kaplan-Meier survival curves were drawn for evaluating the overall survival (OS) of patients classified by different score subgroups. Immunotherapy response and mutation analyses were also conducted. RESULTS In the ANO score model, TNFSF10 was an independent factor for the prognosis of ESCC patients. The area under the curve values of the ANO-TME score model in predicting the OS were 0.638 at 5 years and 0.632 at 7 years. Patients in the ANO low score-TME high score group had a much longer OS than patients in any other ANO-TME score subgroup (p < 0.001), suggesting a higher prognostic value. The differentially expressed genes of the ANO low score-TME high score group were mainly involved in cell adhesion molecules, nucleotide excision repair, the TGF-β signaling pathway and mismatch repair. TP53 (92%), TTN (38%) and NFE2L2 (31%) were the top genes with highest mutant frequency in the ANO low score-TME high score group. CONCLUSIONS A novel prognostic prediction model with high application value was constructed and identified for ESCC patients, which may provide evidence for immunotherapy in the treatment of ESCC.
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Affiliation(s)
- Moyan Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Liang
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Ni Y, Jiang M, Wu Y, Xiao P, Wu A, Xia W, Tang C, Yang X, Tian K, Chen H, Huang R. Anoikis-related CTNND1 is associated with immuno-suppressive tumor microenvironment and predicts unfavorable immunotherapeutic outcome in non-small cell lung cancer. J Cancer 2024; 15:317-331. [PMID: 38169514 PMCID: PMC10758022 DOI: 10.7150/jca.89542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Immunotherapy has greatly changed the treatment of advanced non-small cell lung cancer (NSCLC). Anoikis is a programmed cell death process associated with cancer. However, the correlation between anoikis-related genes and the tumor microenvironment (TME) features and immunotherapeutic outcome in NSCLC has not been fully explored. Methods: The bulk and single-cell transcriptome data of NSCLC were downloaded from TCGA and GEO databases. The distribution of anoikis-related genes on different cell types at the single-cell level was analyzed, and these genes specifically expressed by tumor cells and immunotherapy-related were further extracted. Next, the candidate gene CTNND1 was identified and its correlations with the TME features and immunotherapeutic outcome in NSCLC were explored in multiple public cohorts. Finally, an in-house cohort was used to determine the CTNND1 expression and immuno-correlation in NSCLC. Results: At single-cell atlas, we found that anoikis-related genes expressed specifically in tumor cells of NSCLC. By intersecting anoikis-related genes, immunotherapy-associated genes, and the genes expressed in tumor cells, we obtained a special biomarker CTNND1. In addition, cell-cell communication analysis revealed that CTNND1+ tumor cells communicated with immune subpopulations frequently. Moreover, we found that high expression of CTNND1 was related to immuno-suppressive status of NSCLC. The expression of CTNND1 and its immuno-correlation were also validated, and the results showed that CTNND1 was highly expressed in NSCLC tissues and tumors with high CTNND1 expression accompanied with low CD8+ T cells infiltration. Conclusions: Overall, our study reported that CTNND1 can be considered as a novel biomarker for the predication of immunotherapeutic responses and a potential target for NSCLC therapy.
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Affiliation(s)
- Yingchen Ni
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Mengna Jiang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Yixuan Wu
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Pei Xiao
- Center for Non-Communicable Disease Management, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Anqi Wu
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Weiyi Xia
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Can Tang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Xu Yang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Kai Tian
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Hong Chen
- Department of Respiratory Medicine, Nantong Fourth People's Hospital, Nantong, 226000, China
| | - Rongrong Huang
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
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Wu L, Jin Y, Zhao X, Tang K, Zhao Y, Tong L, Yu X, Xiong K, Luo C, Zhu J, Wang F, Zeng Z, Pan D. Tumor aerobic glycolysis confers immune evasion through modulating sensitivity to T cell-mediated bystander killing via TNF-α. Cell Metab 2023; 35:1580-1596.e9. [PMID: 37506695 DOI: 10.1016/j.cmet.2023.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/09/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023]
Abstract
Metabolic reprogramming toward glycolysis is a hallmark of cancer malignancy. The molecular mechanisms by which the tumor glycolysis pathway promotes immune evasion remain to be elucidated. Here, by performing genome-wide CRISPR screens in murine tumor cells co-cultured with cytotoxic T cells (CTLs), we identified that deficiency of two important glycolysis enzymes, Glut1 (glucose transporter 1) and Gpi1 (glucose-6-phosphate isomerase 1), resulted in enhanced killing of tumor cells by CTLs. Mechanistically, Glut1 inactivation causes metabolic rewiring toward oxidative phosphorylation, which generates an excessive amount of reactive oxygen species (ROS). Accumulated ROS potentiate tumor cell death mediated by tumor necrosis factor alpha (TNF-α) in a caspase-8- and Fadd-dependent manner. Genetic and pharmacological inactivation of Glut1 sensitizes tumors to anti-tumor immunity and synergizes with anti-PD-1 therapy through the TNF-α pathway. The mechanistic interplay between tumor-intrinsic glycolysis and TNF-α-induced killing provides new therapeutic strategies to enhance anti-tumor immunity.
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Affiliation(s)
- Lijian Wu
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiteng Jin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100084, China
| | - Xi Zhao
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Kaiyang Tang
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaoning Zhao
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linjie Tong
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuerong Yu
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ke Xiong
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ce Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100084, China
| | - Jiajun Zhu
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Science (CLS), Beijing 100084, China
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Zexian Zeng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100084, China; Tsinghua-Peking Center for Life Science (CLS), Beijing 100084, China.
| | - Deng Pan
- Department of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Science (CLS), Beijing 100084, China.
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18
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An Z, Liu W, Li W, Wei M, An C. Application of single-cell RNA sequencing in head and neck squamous cell carcinoma. Chin J Cancer Res 2023; 35:331-342. [PMID: 37691894 PMCID: PMC10485914 DOI: 10.21147/j.issn.1000-9604.2023.04.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Single-cell RNA sequencing has been broadly applied to head and neck squamous cell carcinoma (HNSCC) for characterizing the heterogeneity and genomic mutations of HNSCC benefiting from the advantage of single-cell resolution. We summarized most of the current studies and aimed to explore their research methods and ideas, as well as how to transform them into clinical applications. Through single-cell RNA sequencing, we found the differences in tumor cells' expression programs and differentiation tracks. The studies of immune microenvironment allowed us to distinguish immune cell subpopulations, the extensive expression of immune checkpoints, and the complex crosstalk network between immune cells and non-immune cells. For cancer-associated fibroblasts (CAFs), single-cell RNA sequencing had made an irreplaceable contribution to the exploration of their differentiation status, specific CAFs markers, and the interaction with tumor cells and immune cells. In addition, we demonstrated in detail how single-cell RNA sequencing explored the HNSCC epithelial-to-mesenchymal transition (EMT) model and the mechanism of drug resistance, as well as its clinical value.
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Affiliation(s)
- Zhaohong An
- Department of Head & Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wan Liu
- Department of Head & Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen Center, Shenzhen 518000, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Minghui Wei
- Department of Head & Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen Center, Shenzhen 518000, China
| | - Changming An
- Department of Head & Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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19
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Sprenkle NT, Winn NC, Bunn KE, Zhao Y, Park DJ, Giese BG, Karijolich JJ, Ansel KM, Serezani CH, Hasty AH, Pua HH. The miR-23-27-24 clusters drive lipid-associated macrophage proliferation in obese adipose tissue. Cell Rep 2023; 42:112928. [PMID: 37542720 PMCID: PMC10712211 DOI: 10.1016/j.celrep.2023.112928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023] Open
Abstract
Identifying molecular circuits that control adipose tissue macrophage (ATM) function is necessary to understand how ATMs contribute to tissue homeostasis and obesity-induced insulin resistance. In this study, we find that mice with a myeloid-specific knockout of the miR-23-27-24 clusters of microRNAs (miRNAs) gain less weight on a high-fat diet but exhibit worsened glucose and insulin tolerance. Analysis of ATMs from these mice shows selectively reduced numbers and proliferation of a recently reported subset of lipid-associated CD9+Trem2+ ATMs (lipid-associated macrophages [LAMs]). Leveraging the role of miRNAs to control networks of genes, we use RNA sequencing (RNA-seq), functional screens, and biochemical assays to identify candidate target transcripts that regulate proliferation-associated signaling. We determine that miR-23 directly targets the mRNA of Eif4ebp2, a gene that restricts protein synthesis and proliferation in macrophages. Altogether, our study demonstrates that control of proliferation of a protective subset of LAMs by noncoding RNAs contributes to protection against diet-induced obesity metabolic dysfunction.
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Affiliation(s)
- Neil T Sprenkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nathan C Winn
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kaitlyn E Bunn
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Deborah J Park
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brenna G Giese
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John J Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanerbilt-Ingram Cancer Center, Nashville, TN, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - C Henrique Serezani
- Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyssa H Hasty
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Heather H Pua
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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20
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Zhang H, Lu X, Lu B, Chen L. scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data. Cancers (Basel) 2023; 15:4277. [PMID: 37686554 PMCID: PMC10486867 DOI: 10.3390/cancers15174277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Single-cell transcriptome analysis has fundamentally changed biological research by allowing higher-resolution computational analysis of individual cells and subsets of cell types. However, few methods have met the need to recognize and quantify the underlying cellular programs that determine the specialization and differentiation of the cell types. METHODS In this study, we present scGEM, a nested tree-structured nonparametric Bayesian model, to reveal the gene co-expression modules (GEMs) reflecting transcriptome processes in single cells. RESULTS We show that scGEM can discover shared and specialized transcriptome signals across different cell types using peripheral blood mononuclear single cells and early brain development single cells. scGEM outperformed other methods in perplexity and topic coherence (p < 0.001) on our simulation data. Larger datasets, deeper trees and pre-trained models are shown to be positively associated with better scGEM performance. The GEMs obtained from triple-negative breast cancer single cells exhibited better correlations with lymphocyte infiltration (p = 0.009) and the cell cycle (p < 0.001) than other methods in additional validation on the bulk RNAseq dataset. CONCLUSIONS Altogether, we demonstrate that scGEM can be used to model the hidden cellular functions of single cells, thereby unveiling the specialization and generalization of transcriptomic programs across different types of cells.
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Affiliation(s)
- Han Zhang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Binfeng Lu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Lujia Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
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21
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Lu T, Xu R, Wang C, Zhou X, Parra-Medina R, Díaz-Peña R, Peng B, Zhang L. Bioinformatics analysis and single-cell RNA sequencing: elucidating the ubiquitination pathways and key enzymes in lung adenocarcinoma. J Thorac Dis 2023; 15:3885-3907. [PMID: 37559628 PMCID: PMC10407523 DOI: 10.21037/jtd-23-795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a prevalent subtype of lung cancer associated with high mortality rates. We aimed to utilize single-cell multiomics analysis to identify the key molecules involved in ubiquitination modification, which plays a role in LUAD development and progression. METHODS We use a systematic approach to analyze LUAD-related single-cell and bulk transcriptome datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Single-cell RNA sequencing (scRNA-seq) data were normalized, clustered, and annotated with the Seurat package in R. InferCNV was used to distinguish malignant from epithelial cells, and AUCell evaluated the area under the curve (AUC) score of ubiquitination-related enzymes. Survival and differential analyses identified significant molecular markers associated with ubiquitination. PSMD14 expression was confirmed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot assays, and its knockdown cell lines were assessed for effects on cellular processes and tumor formation in mice. PSMD14's interacting proteins were predicted, and its impact on AGR2 protein half-life and ubiquitination was evaluated. Rescue experiments involving PSMD14 overexpression and AGR2 silencing assessed their impact on malignant behaviors. RESULTS By means of single-cell sequencing analysis, we probed the ubiquitination modification landscape in the LUAD microenvironment. Malignant cells had elevated scores for enzymes and ubiquitin-binding domains compared to normal epithelial cells, with 53 ubiquitination-related molecules showing prognostic disparities. FGR, PSMD14, and ZBTB16 were identified as genes with prognostic significance, with PSMD14 showing higher expression in epithelial and malignant cells. Two missense mutation sites were identified in PSMD14, which had a high copy number amplification ratio and positive correlation with messenger RNA (mRNA) expression. PSMD14 expression and tumor stage were found to be independent prognostic factors, and interfering with PSMD14 expression reduced the malignant behavior of LUAD cells. PSMD14 was found to bind to AGR2 protein and reduce its ubiquitination, leading to increased AGR2 stability. Knockdown of AGR2 inhibited the enhancement of cell viability, invasion, and migration resulting from PSMD14 overexpression. CONCLUSIONS This study examined ubiquitination modifications in LUAD using sequencing data, identifying PSMD14's critical role in malignancy regulation and its potential as a prognostic and therapeutic biomarker. These insights enhance understanding of LUAD mechanisms and treatment.
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Affiliation(s)
- Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
| | - Chenghao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
| | - Xiang Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
| | - Rafael Parra-Medina
- Department of Pathology, Fundación Universitaria de Ciencias de la Salud, Hospital San José, Bogotá, Colombia
- Department of Pathology, National Cancer Institute (INC), Bogotá, Colombia
| | - Roberto Díaz-Peña
- Fundación Pública Galega de Medicina Xenómica, SERGAS, Grupo de Medicina Xenómica-USC, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Harbin Medical University, Harbin, China
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22
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Song Q, Ruiz J, Xing F, Lo HW, Craddock L, Pullikuth AK, Miller LD, Soike MH, O'Neill SS, Watabe K, Chan MD, Su J. Single-cell sequencing reveals the landscape of the human brain metastatic microenvironment. Commun Biol 2023; 6:760. [PMID: 37479733 PMCID: PMC10362065 DOI: 10.1038/s42003-023-05124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Brain metastases is the most common intracranial tumor and account for approximately 20% of all systematic cancer cases. It is a leading cause of death in advanced-stage cancer, resulting in a five-year overall survival rate below 10%. Therefore, there is a critical need to identify effective biomarkers that can support frequent surveillance and promote efficient drug guidance in brain metastasis. Recently, the remarkable breakthroughs in single-cell RNA-sequencing (scRNA-seq) technology have advanced our insights into the tumor microenvironment (TME) at single-cell resolution, which offers the potential to unravel the metastasis-related cellular crosstalk and provides the potential for improving therapeutic effects mediated by multifaceted cellular interactions within TME. In this study, we have applied scRNA-seq and profiled 10,896 cells collected from five brain tumor tissue samples originating from breast and lung cancers. Our analysis reveals the presence of various intratumoral components, including tumor cells, fibroblasts, myeloid cells, stromal cells expressing neural stem cell markers, as well as minor populations of oligodendrocytes and T cells. Interestingly, distinct cellular compositions are observed across different samples, indicating the influence of diverse cellular interactions on the infiltration patterns within the TME. Importantly, we identify tumor-associated fibroblasts in both our in-house dataset and external scRNA-seq datasets. These fibroblasts exhibit high expression of type I collagen genes, dominate cell-cell interactions within the TME via the type I collagen signaling axis, and facilitate the remodeling of the TME to a collagen-I-rich extracellular matrix similar to the original TME at primary sites. Additionally, we observe M1 activation in native microglial cells and infiltrated macrophages, which may contribute to a proinflammatory TME and the upregulation of collagen type I expression in fibroblasts. Furthermore, tumor cell-specific receptors exhibit a significant association with patient survival in both brain metastasis and native glioblastoma cases. Taken together, our comprehensive analyses identify type I collagen-secreting tumor-associated fibroblasts as key mediators in metastatic brain tumors and uncover tumor receptors that are potentially associated with patient survival. These discoveries provide potential biomarkers for effective therapeutic targets and intervention strategies.
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Affiliation(s)
- Qianqian Song
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jimmy Ruiz
- Hematology & Oncology, Department of Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
- W.G. (Bill) Hefner Department of Veteran Affairs Medical Center, Salisbury, NC, USA.
| | - Fei Xing
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Hui-Wen Lo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lou Craddock
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Ashok K Pullikuth
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michael H Soike
- Hazlerig-Salter Department of Radiation Oncology, University of Alabama-Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Stacey S O'Neill
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michael D Chan
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
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23
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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24
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Sahu A, Wang X, Munson P, Klomp JP, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JA, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KT. Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha. Cancer Discov 2023; 13:672-701. [PMID: 36745048 PMCID: PMC9975674 DOI: 10.1158/2159-8290.cd-22-0244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 02/07/2023]
Abstract
Drugs that kill tumors through multiple mechanisms have the potential for broad clinical benefits. Here, we first developed an in silico multiomics approach (BipotentR) to find cancer cell-specific regulators that simultaneously modulate tumor immunity and another oncogenic pathway and then used it to identify 38 candidate immune-metabolic regulators. We show the tumor activities of these regulators stratify patients with melanoma by their response to anti-PD-1 using machine learning and deep neural approaches, which improve the predictive power of current biomarkers. The topmost identified regulator, ESRRA, is activated in immunotherapy-resistant tumors. Its inhibition killed tumors by suppressing energy metabolism and activating two immune mechanisms: (i) cytokine induction, causing proinflammatory macrophage polarization, and (ii) antigen-presentation stimulation, recruiting CD8+ T cells into tumors. We also demonstrate a wide utility of BipotentR by applying it to angiogenesis and growth suppressor evasion pathways. BipotentR (http://bipotentr.dfci.harvard.edu/) provides a resource for evaluating patient response and discovering drug targets that act simultaneously through multiple mechanisms. SIGNIFICANCE BipotentR presents resources for evaluating patient response and identifying targets for drugs that can kill tumors through multiple mechanisms concurrently. Inhibition of the topmost candidate target killed tumors by suppressing energy metabolism and effects on two immune mechanisms. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, Colorado
| | - Xiaoman Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Phillip Munson
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | - Xiaoqing Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Cardiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shengqing Stan Gu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ya Han
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gege Qian
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Phillip Nicol
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chenfei Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | - Bas Jansen
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | | | - Jaap Lemmers
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | - Mark Musters
- Lead Pharma, Kloosterstraat, Oss, the Netherlands
| | | | | | | | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, Massachusetts
| | - Dejan Juric
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Clifford A. Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David E. Fisher
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Keith T. Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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25
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The Recurrent-Specific Regulation Network of Prognostic Stemness-Related Signatures in Low-Grade Glioma. DISEASE MARKERS 2023; 2023:2243928. [PMID: 36703644 PMCID: PMC9873439 DOI: 10.1155/2023/2243928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 01/19/2023]
Abstract
Gliomas including astrocytomas, oligodendrogliomas, mixed oligoastrocytic, and mixed glioneuronal tumors are an important group of brain tumors. Based on the 2016 WHO classification for tumors in the central nervous system, gliomas were classified into four grades, from I to IV, and brain lower grade glioma (LGG) consists of grade II and grade III. Patients with LGG may undergo recurrence, which makes clinical treatment tough. Stem cell-like features of cancer cells play a key role in tumor's biological behaviors, including tumorigenesis, development, and clinical prognosis. In this article, we quantified the stemness feature of cancer cells using the mRNA stemness index (mRNAsi) and identified stemness-related key genes based on correlation with mRNAsi. Besides, hallmark gene sets and translate factors (TFs) which were highly related to stemness-related key genes were identified. Therefore, a recurrency-specific network was constructed and a potential regulation pathway was identified. Several online databases, assay for transposase-accessible chromatin using sequencing (ATAC-seq), single-cell sequencing analysis, and immunohistochemistry were utilized to validate the scientific hypothesis. Finally, we proposed that aurora kinase A (AURKA), positively regulated by Non-SMC Condensin I Complex Subunit G (NCAPG), promoted E2F target pathway in LGG, which played an important role in LGG recurrence.
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Yang T, Zhang S, Yuan H, Wang Y, Cai L, Chen H, Wang X, Song D, Wang X, Guo Z, Wang X. Platinum-Based TREM2 Inhibitor Suppresses Tumors by Remodeling the Immunosuppressive Microenvironment. Angew Chem Int Ed Engl 2023; 62:e202213337. [PMID: 36259513 DOI: 10.1002/anie.202213337] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 11/07/2022]
Abstract
Triggering receptor expressed on myeloid cells-2 (TREM2) is a key pro-tumorigenic marker of tumor-infiltrating macrophages, showing potent immunosuppressive activity in tumor microenvironment. A platinum(IV) complex OPA derived from oxaliplatin (OP) and artesunate (ART) exhibited direct cytotoxicity against human colon cancer cells and immunomodulatory activity to inhibit TREM2 on macrophages in vitro and vivo. Furthermore, OPA deterred the tumor growth in mouse models bearing MC38 colorectal tumor by reducing the number of CD206+ and CX3 CR1+ immunosuppressive macrophages; it also promoted the expansion and infiltration of immunostimulatory dendritic, cytotoxic T, and natural killer cells. OPA is the first small-molecular TREM2 inhibitor capable of relieving immunosuppressive tumor microenvironment and enhancing chemical anticancer efficiency of a platinum drug, thus showing typical characteristics of a chemoimmunotherapeutic agent.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
| | - Shuren Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
| | - Hao Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Ying Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, P. R. China
| | - Linxiang Cai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, P. R. China
| | - Hanhua Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, P. R. China
| | - Xiaoyu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Xiaohui Wang
- Institute of Chemical Biology and Functional Molecules, State Key Laboratory of Materials-Oriented Chemical Engineering, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
| | - Xiaoyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, P. R. China
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Schaafsma E, Croteau W, Mohamed E, Nowak EC, Smits NC, Deng J, Sarde A, Webber CA, Rabadi D, Cheng C, Noelle R, Lines JL. VISTA Targeting of T-cell Quiescence and Myeloid Suppression Overcomes Adaptive Resistance. Cancer Immunol Res 2023; 11:38-55. [PMID: 36260656 PMCID: PMC10544831 DOI: 10.1158/2326-6066.cir-22-0116] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/18/2022] [Accepted: 10/14/2022] [Indexed: 01/05/2023]
Abstract
V domain immunoglobulin suppressor of T-cell activation (VISTA) is a premier target for cancer treatment due to its broad expression in many cancer types and enhanced expression upon development of adaptive immune checkpoint resistance. In the CT26 colorectal cancer model, monotherapy of small tumors with anti-VISTA resulted in slowed tumor growth. In a combination therapy setting, large CT26 tumors showed complete adaptive resistance to anti-PD-1/CTLA-4, but inclusion of anti-VISTA led to rejection of half the tumors. Mechanisms of enhanced antitumor immunity were investigated using single-cell RNA sequencing (scRNA-seq), multiplex image analysis, and flow cytometry of the tumor immune infiltrate. In both treatment models, anti-VISTA upregulated stimulated antigen presentation pathways and reduced myeloid-mediated suppression. Imaging revealed an anti-VISTA stimulated increase in contacts between T cells and myeloid cells, further supporting the notion of increased antigen presentation. scRNA-seq of tumor-specific CD8+ T cells revealed that anti-VISTA therapy induced T-cell pathways highly distinct from and complementary to those induced by anti-PD-1 therapy. Whereas anti-CTLA-4/PD-1 expanded progenitor exhausted CD8+ T-cell subsets, anti-VISTA promoted costimulatory genes and reduced regulators of T-cell quiescence. Notably, this is the first report of a checkpoint regulator impacting CD8+ T-cell quiescence, and the first indication that quiescence may be a target in the context of T-cell exhaustion and in cancer. This study builds a foundation for all future studies on the role of anti-VISTA in the development of antitumor immunity and provides important mechanistic insights that strongly support use of anti-VISTA to overcome the adaptive resistance seen in contemporary treatments involving PD-1 and/or CTLA-4. See related Spotlight by Wei, p. 3.
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Affiliation(s)
- Evelien Schaafsma
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Walburga Croteau
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - ElTanbouly Mohamed
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Elizabeth C. Nowak
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Nicole C. Smits
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jie Deng
- University of California, Los Angeles. Department of Radiation Oncology
| | - Aurelien Sarde
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Dina Rabadi
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Chao Cheng
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Randolph Noelle
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - J. Louise Lines
- Department of Microbiology and Immunology, Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Sakref C, Bendriss-Vermare N, Valladeau-Guilemond J. Phenotypes and Functions of Human Dendritic Cell Subsets in the Tumor Microenvironment. Methods Mol Biol 2023; 2618:17-35. [PMID: 36905506 DOI: 10.1007/978-1-0716-2938-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Dendritic cells (DCs) play a key role in the antitumor immunity, as they are at the interface of innate and adaptive immunity. This important task can only be performed thanks to the broad range of mechanisms that DCs can perform to activate other immune cells. As DCs are well known for their outstanding capacity to prime and activate T cells through antigen presentation, DCs were intensively investigated during the past decades. Numerous studies have identified new DC subsets, leading to a large variety of subsets commonly separated into cDC1, cDC2, pDCs, mature DCs, Langerhans cells, monocyte-derived DCs, Axl-DCs, and several other subsets. Here, we review the specific phenotypes, functions, and localization within the tumor microenvironment (TME) of human DC subsets thanks to flow cytometry and immunofluorescence but also with the help of high-output technologies such as single-cell RNA sequencing and imaging mass cytometry (IMC).
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Affiliation(s)
- Candice Sakref
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- LabEx DEVweCAN, Lyon, France
| | - Nathalie Bendriss-Vermare
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- LabEx DEVweCAN, Lyon, France
- Laboratoire d'Immunothérapie des Cancers de Lyon (LICL), Lyon, France
| | - Jenny Valladeau-Guilemond
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.
- LabEx DEVweCAN, Lyon, France.
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TREM2 knockdown improves the therapeutic effect of PD-1 blockade in hepatocellular carcinoma. Biochem Biophys Res Commun 2022; 636:140-146. [DOI: 10.1016/j.bbrc.2022.10.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2022]
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30
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Qian Y, Yang T, Liang H, Deng M. Myeloid checkpoints for cancer immunotherapy. Chin J Cancer Res 2022; 34:460-482. [PMID: 36398127 PMCID: PMC9646457 DOI: 10.21147/j.issn.1000-9604.2022.05.07] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2023] Open
Abstract
Myeloid checkpoints are receptors on the myeloid cell surface which can mediate inhibitory signals to modulate anti-tumor immune activities. They can either inhibit cellular phagocytosis or suppress T cells and are thus involved in the pathogenesis of various diseases. In the tumor microenvironment, besides killing tumor cells by phagocytosis or activating anti-tumor immunity by tumor antigen presentation, myeloid cells could execute pro-tumor efficacies through myeloid checkpoints by interacting with counter-receptors on other immune cells or cancer cells. In summary, myeloid checkpoints may be promising therapeutic targets for cancer immunotherapy.
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Affiliation(s)
- Yixin Qian
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, China
| | - Ting Yang
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, China
| | - Huan Liang
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, China
| | - Mi Deng
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, China
- Peking University Cancer Hospital & Institute, Peking University, Beijing 100142, China
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31
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Decoding Single-cell Landscape and Intercellular Crosstalk in the Transplanted Liver. Transplantation 2022; 107:890-902. [PMID: 36413145 DOI: 10.1097/tp.0000000000004365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Liver transplantation (LT) is the most effective treatment for various end-stage liver diseases. However, the cellular complexity and intercellular crosstalk of the transplanted liver have constrained analyses of graft reconstruction after LT. METHODS We established an immune-tolerated orthotopic LT mouse model to understand the physiological process of graft recovery and intercellular crosstalk. We employed single-cell RNA sequencing and cytometry by time-of-flight to comprehensively reveal the cellular landscape. RESULTS We identified an acute and stable phase during perioperative graft recovery. Using single-cell technology, we made detailed annotations of the cellular landscape of the transplanted liver and determined dynamic modifications of these cells during LT. We found that 96% of graft-derived immune cells were replaced by recipient-derived cells from the preoperative to the stable phase. However, CD206 + MerTK + macrophages and CD49a + CD49b - natural killer cells were composed of both graft and recipient sources even in the stable phase. Intriguingly, the transcriptional profiles of these populations exhibited tissue-resident characteristics, suggesting that recipient-derived macrophages and natural killer cells have the potential to differentiate into 'tissue-resident cells' after LT. Furthermore, we described the transcriptional characteristics of these populations and implicated their role in regulating the metabolic and immune remodeling of the transplanted liver. CONCLUSIONS In summary, this study delineated a cell atlas (type-proportion-source-time) of the transplanted liver and shed light on the physiological process of graft reconstruction and graft-recipient crosstalk.
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Hao B, Zhang Z, Lu Z, Xiong J, Fan T, Song C, He R, Zhang L, Pan S, Li D, Meng H, Lin W, Luo B, Yang J, Li N, Geng Q. Single-cell RNA sequencing analysis revealed cellular and molecular immune profiles in lung squamous cell carcinoma. Transl Oncol 2022; 27:101568. [PMID: 36270103 PMCID: PMC9586982 DOI: 10.1016/j.tranon.2022.101568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/05/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Although breakthroughs have been made in the treatment of non-small cell lung cancer, there are only a few choices for advanced-stage or recurrent lung squamous cell carcinoma (LUSC) patients. In our study, we identified 7 major cell types in thedepicted the immunolandscape of LUSC microenvironment using single-cell RNA sequencing. We found that an immunosuppressive receptor, T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT), was highly expressed by regulatory T cells (Tregs) and exhausted CD8+T cells, suggesting that upregulation of TIGIT might promote an immunosuppressive microenvironment and inhibit the cytotoxic ability of CD8+T cells. We also identified tumor-associated neutrophil (TAN), characterized by CXCR2, CSF3R and CXCL8, in the tumor region, and TANs upregulated the expression of interleukin 1 receptor antagonist (IL1RN) which suggested that TAN might exert an immunosuppressive role via expressing IL1RN. Furthermore, the number of SPP1+ macrophages(SPP1+M) significantly increased in tumor microenvirnment, which was correlated with the poor survival of patients. Additionally, regulatory networks based on SPP1+M revealed that the disparities of several ligand-receptor pairs existed between tumor and normal tissues. Among these pairs, SPP1-CD44 showed the most interactions between SPP1+M and other cell types. Our results provided deep insight into the immune landscape of LUSC and an essential resource for drug discovery in the future.
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Affiliation(s)
- Bo Hao
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ziyao Zhang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zilong Lu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Juan Xiong
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tao Fan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ruyuan He
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lin Zhang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Shize Pan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Donghang Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Heng Meng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Weichen Lin
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Bin Luo
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinfeng Yang
- Department of Pathology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China,Corresponding author.
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Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nat Commun 2022; 13:6118. [PMID: 36253379 PMCID: PMC9574176 DOI: 10.1038/s41467-022-33758-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., single-cell RNA sequencing, scRNA-seq, single-cell assay for transposase-accessible chromatin use sequencing, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX's advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build upon previous scientific insights.
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34
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Wang Y, Gao Y, Zhang C, Yue J, Wang R, Liu H, Yang X, Zhang Y, Yang R. Tumor Environment Promotes Lnc57Rik-Mediated Suppressive Function of Myeloid-Derived Suppressor Cells. THE JOURNAL OF IMMUNOLOGY 2022; 209:1401-1413. [DOI: 10.4049/jimmunol.2200195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022]
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35
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Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM. Single cell RNA-sequencing: A powerful yet still challenging technology to study cellular heterogeneity. Bioessays 2022; 44:e2200084. [PMID: 36068142 DOI: 10.1002/bies.202200084] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/11/2022]
Abstract
Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic 'average' cannot outright be used as representative of the 'average cell'. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single-cell RNA sequencing (scRNA-Seq) enables the comparison of the transcriptomes of individual cells. This provides high-resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context-specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA-Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA-Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research.
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Affiliation(s)
- May Ke
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Badran Elshenawy
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Helen Sheldon
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Anjali Arora
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK.,Department of Computing Sciences, Bocconi University, Milano, Italy.,Institute for Data Science and Analytics, Bocconi University, Milano, Italy
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Luo Y, Deng X, Que J, Li Z, Xie W, Dai G, Chen L, Wang H. Cell Trajectory-Related Genes of Lung Adenocarcinoma Predict Tumor Immune Microenvironment and Prognosis of Patients. Front Oncol 2022; 12:911401. [PMID: 35924143 PMCID: PMC9339705 DOI: 10.3389/fonc.2022.911401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/23/2022] [Indexed: 01/21/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer which typically exhibits a diverse progression trajectory. Our study sought to explore the cell differentiation trajectory of LUAD and its clinical relevance. Methods Utilizing a single-cell RNA-sequencing dataset (GSE117570), we identified LUAD cells of distinct differential status along with differentiation-related genes (DRGs). DRGs were applied to the analysis of bulk-tissue RNA-sequencing dataset (GSE72094) to classify tumors into different subtypes, whose clinical relevance was further analyzed. DRGs were also applied to gene co-expression network analysis (WGCNA) using another bulk-tissue RNA-sequencing dataset (TCGA-LUAD). Genes from modules that demonstrated a significant correlation with clinical traits and were differentially expressed between normal tissue and tumors were identified. Among these, genes with significant prognostic relevance were used for the development of a prognostic nomogram, which was tested on TCGA-LUAD dataset and validated in GSE72094. Finally, CCK-8, EdU, cell apoptosis, cell colony formation, and Transwell assays were used to verify the functions of the identified genes. Results Four clusters of cells with distinct differentiation status were characterized, whose DRGs were predominantly correlated with pathways of immune regulation. Based on DRGs, tumors could be clustered into four subtypes associated with distinct immune microenvironment and clinical outcomes. DRGs were categorized into four modules. A total of nine DRGs (SFTPB, WFDC2, HLA-DPA1, TIMP1, MS4A7, HLA-DQA1, VCAN, KRT8, and FABP5) with most significant survival-predicting power were integrated to develop a prognostic model, which outperformed the traditional parameters in predicting clinical outcomes. Finally, we verified that knockdown of WFDC2 inhibited proliferation, migration, and invasion but promoted the apoptosis of A549 cells in vitro. Conclusion The cellular composition and cellular differentiation status of tumor mass can predict the clinical outcomes of LUAD patients. It also plays an important role in shaping the tumor immune microenvironment.
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Affiliation(s)
- Yu Luo
- Department of Thoracic Surgery, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Xiaheng Deng
- Department of Thoracic Surgery, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Zhihua Li
- Department of Thoracic Surgery, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Weiping Xie
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Guanqun Dai
- Department of General Practice, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
- *Correspondence: Liang Chen, ; Hong Wang, ;
| | - Hong Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
- *Correspondence: Liang Chen, ; Hong Wang, ;
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Geng A, Flint E, Bernsmeier C. Plasticity of monocytes and macrophages in cirrhosis of the liver. FRONTIERS IN NETWORK PHYSIOLOGY 2022; 2:937739. [PMID: 36926073 PMCID: PMC10013015 DOI: 10.3389/fnetp.2022.937739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/27/2022] [Indexed: 06/06/2023]
Abstract
Cirrhosis of the liver is a systemic condition with raising prevalence worldwide. Patients with cirrhosis are highly susceptible to develop bacterial infections leading to acute decompensation and acute-on-chronic liver failure both associated with a high morbidity and mortality and sparse therapeutic options other than transplantation. Mononuclear phagocytes play a central role in innate immune responses and represent a first line of defence against pathogens. Their function includes phagocytosis, killing of bacteria, antigen presentation, cytokine production as well as recruitment and activation of immune effector cells. Liver injury and development of cirrhosis induces activation of liver resident Kupffer cells and recruitment of monocytes to the liver. Damage- and pathogen-associated molecular patterns promote systemic inflammation which involves multiple compartments besides the liver, such as the circulation, gut, peritoneal cavity and others. The function of circulating monocytes and tissue macrophages is severely impaired and worsens along with cirrhosis progression. The underlying mechanisms are complex and incompletely understood. Recent 'omics' technologies help to transform our understanding of cellular diversity and function in health and disease. In this review we point out the current state of knowledge on phenotypical and functional changes of monocytes and macrophages during cirrhosis evolution in different compartments and their role in disease progression. We also discuss the value of potential prognostic markers for cirrhosis-associated immuneparesis, and future immunotherapeutic strategies that may reduce the need for transplantation and death.
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Affiliation(s)
- Anne Geng
- Translational Hepatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel and University Centre for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Emilio Flint
- Translational Hepatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel and University Centre for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Christine Bernsmeier
- Translational Hepatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel and University Centre for Gastrointestinal and Liver Diseases, Basel, Switzerland
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Joshi S, Sharabi A. Targeting myeloid-derived suppressor cells to enhance natural killer cell-based immunotherapy. Pharmacol Ther 2022; 235:108114. [DOI: 10.1016/j.pharmthera.2022.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 12/09/2022]
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Njock MS, O'Grady T, Nivelles O, Lion M, Jacques S, Cambier M, Herkenne S, Muller F, Christian A, Remacle C, Guiot J, Rahmouni S, Dequiedt F, Struman I. Endothelial extracellular vesicles promote tumour growth by tumour-associated macrophage reprogramming. J Extracell Vesicles 2022; 11:e12228. [PMID: 35656866 PMCID: PMC9164145 DOI: 10.1002/jev2.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 04/19/2022] [Accepted: 04/30/2022] [Indexed: 12/21/2022] Open
Abstract
Tumour-derived extracellular vesicles (EVs) participate in tumour progression by deregulating various physiological processes including angiogenesis and inflammation. Here we report that EVs released by endothelial cells in a mammary tumour environment participate in the recruitment of macrophages within the tumour, leading to an immunomodulatory phenotype permissive for tumour growth. Using RNA-Seq approaches, we identified several microRNAs (miRNAs) found in endothelial EVs sharing common targets involved in the regulation of the immune system. To further study the impact of these miRNAs in a mouse tumour model, we focused on three miRNAs that are conserved between humans and mouse, that is, miR-142-5p, miR-183-5p and miR-222-3p. These miRNAs are released from endothelial cells in a tumour microenvironment and are transferred via EVs to macrophages. In mouse mammary tumour models, treatment with EVs enriched in these miRNAs leads to a polarization of macrophages toward an M2-like phenotype, which in turn promotes tumour growth.
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Affiliation(s)
- Makon-Sébastien Njock
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Tina O'Grady
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Olivier Nivelles
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Michelle Lion
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Sophie Jacques
- Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Maureen Cambier
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Stephanie Herkenne
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Florian Muller
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Aurélie Christian
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Claire Remacle
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium.,Department of Pneumology, GIGA Research Centre, University and CHU of Liège, Liège, Belgium
| | - Julien Guiot
- Department of Pneumology, GIGA Research Centre, University and CHU of Liège, Liège, Belgium
| | - Souad Rahmouni
- Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA Research Centre, University of Liège, Liège, Belgium
| | - Franck Dequiedt
- Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Ingrid Struman
- Laboratory of Molecular Angiogenesis, GIGA Research Centre, University of Liège, Liège, Belgium
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Li P, Ma C, Li J, You S, Dang L, Wu J, Hao Z, Li J, Zhi Y, Chen L, Sun S. Proteomic characterization of four subtypes of M2 macrophages derived from human THP-1 cells. J Zhejiang Univ Sci B 2022; 23:407-422. [PMID: 35557041 DOI: 10.1631/jzus.b2100930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Macrophages are widely distributed immune cells that contribute to tissue homeostasis. Human THP-1 cells have been widely used in various macrophage-associated studies, especially those involving pro-inflammatory M1 and anti-inflammatory M2 phenotypes. However, the molecular characterization of four M2 subtypes (M2a, M2b, M2c, and M2d) derived from THP-1 has not been fully investigated. In this study, we systematically analyzed the protein expression profiles of human THP-1-derived macrophages (M0, M1, M2a, M2b, M2c, and M2d) using quantitative proteomics approaches. The commonly and specially regulated proteins of the four M2 subtypes and their potential biological functions were further investigated. The results showed that M2a and M2b, and M2c and M2d have very similar protein expression profiles. These data could serve as an important resource for studies of macrophages using THP-1 cells, and provide a reference to distinguish different M2 subtypes in macrophage-associated diseases for subsequent clinical research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shisheng Sun
- College of Life Science, Northwest University, Xi'an 710069, China.
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Zhang Z, Wang ZX, Chen YX, Wu HX, Yin L, Zhao Q, Luo HY, Zeng ZL, Qiu MZ, Xu RH. Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response. Genome Med 2022; 14:45. [PMID: 35488273 PMCID: PMC9052621 DOI: 10.1186/s13073-022-01050-w] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the potential culprit in ICI resistance, but direct clinical evidence is lacking. METHODS Publicly available scRNA-Seq datasets derived from ICI-treated patients were collected and analyzed to elucidate the association between cancer stemness and ICI response. A novel stemness signature (Stem.Sig) was developed and validated using large-scale pan-cancer data, including 34 scRNA-Seq datasets, The Cancer Genome Atlas (TCGA) pan-cancer cohort, and 10 ICI transcriptomic cohorts. The therapeutic value of Stem.Sig genes was further explored using 17 CRISPR datasets that screened potential immunotherapy targets. RESULTS Cancer stemness, as evaluated by CytoTRACE, was found to be significantly associated with ICI resistance in melanoma and basal cell carcinoma (both P < 0.001). Significantly negative association was found between Stem.Sig and anti-tumor immunity, while positive correlations were detected between Stem.Sig and intra-tumoral heterogenicity (ITH) / total mutational burden (TMB). Based on this signature, machine learning model predicted ICI response with an AUC of 0.71 in both validation and testing set. Remarkably, compared with previous well-established signatures, Stem.Sig achieved better predictive performance across multiple cancers. Moreover, we generated a gene list ranked by the average effect of each gene to enhance tumor immune response after genetic knockout across different CRISPR datasets. Then we matched Stem.Sig to this gene list and found Stem.Sig significantly enriched 3% top-ranked genes from the list (P = 0.03), including EMC3, BECN1, VPS35, PCBP2, VPS29, PSMF1, GCLC, KXD1, SPRR1B, PTMA, YBX1, CYP27B1, NACA, PPP1CA, TCEB2, PIGC, NR0B2, PEX13, SERF2, and ZBTB43, which were potential therapeutic targets. CONCLUSIONS We revealed a robust link between cancer stemness and immunotherapy resistance and developed a promising signature, Stem.Sig, which showed increased performance in comparison to other signatures regarding ICI response prediction. This signature could serve as a competitive tool for patient selection of immunotherapy. Meanwhile, our study potentially paves the way for overcoming immune resistance by targeting stemness-associated genes.
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Affiliation(s)
- Zhen Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Zi-Xian Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yan-Xing Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Hao-Xiang Wu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Ling Yin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Qi Zhao
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Zhao-Lei Zeng
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China
| | - Miao-Zhen Qiu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China.
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, 510060, P. R. China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, P. R. China.
- Laboratory of Artificial Intelligence and Data Science, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
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Zhu Y, Fu D, Shi Q, Shi Z, Dong L, Yi H, Liu Z, Feng Y, Liu Q, Fang H, Cheng S, Wang L, Tian Q, Xu P, Zhao W. Oncogenic Mutations and Tumor Microenvironment Alterations of Older Patients With Diffuse Large B-Cell Lymphoma. Front Immunol 2022; 13:842439. [PMID: 35401516 PMCID: PMC8990904 DOI: 10.3389/fimmu.2022.842439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The incidence of diffuse large B-cell lymphoma (DLBCL) increases by age and older DLBCL are commonly related to poor prognosis. However, the clinical and biological features of older DLBCL patients remain to be determined. A total of 2,445 patients with newly diagnosed DLBCL were enrolled for clinical data analysis according to age at diagnosis, with tumor samples of 1,150 patients assessed by DNA sequencing and 385 patients by RNA sequencing. Older DLBCL presented advanced disease stage, elevated serum lactate dehydrogenase, poor performance status, multiple extranodal involvement, high percentage of double expressor subtype, and adverse clinical outcome. According to molecular features, age was positively correlated with the oncogenic mutations of PIM1, MYD88, BTG2, CD79B, TET2, BTG1, CREBBP, TBL1XR1, and with the MYD88-like genetic subtype. These oncogenic mutations were involved in B-cell receptor/NF-κB signaling, B-cell differentiation, and histone acetylation based on biological functions. Older DLBCL also manifested reduction in CD4+ naïve T and CD8+ naïve T cells, and also increased recruitment of exhausted T cells and macrophages, leading to immunosuppressive tumor microenvironment. Our work thus contributes to the understanding of aging-related oncogenic mutations and tumor microenvironment alterations in lymphoma progression, and may provide new insights to mechanism-based targeted therapy in DLBCL.
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Affiliation(s)
- Yue Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Di Fu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Shi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ziyang Shi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongmei Yi
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenhua Liu
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Shanghai, China
| | - Qiang Tian
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengpeng Xu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Weili Zhao, ; Pengpeng Xu,
| | - Weili Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Shanghai, China
- *Correspondence: Weili Zhao, ; Pengpeng Xu,
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Immunosuppressive TREM2(+) macrophages are associated with undesirable prognosis and responses to anti-PD-1 immunotherapy in non-small cell lung cancer. Cancer Immunol Immunother 2022; 71:2511-2522. [PMID: 35278107 DOI: 10.1007/s00262-022-03173-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Immune checkpoint blockade (ICB) has been improving patient outcomes of non-small cell lung cancer (NSCLC), but its effectiveness is highly subjective to individual tumor microenvironment. As dominant immune cells in NSCLC, tumor-associated macrophages (TAMs) display high diversity and plasticity. This study aims to find crucial TAM subtypes associated with ICB response in NSCLC. MATERIALS AND METHODS Large cohorts of NSCLC patients from The Cancer Genome Atlas and a single-cell sequencing dataset were integrated to illustrate immunosuppressive phenotypes of TAMs, followed by experimental verification. 341 NSCLC surgical samples and 40 tissue samples of NSCLC patients who received ICB treatment were collected to state the clinical importance of TAMs. RESULTS We identified a TREM2 positive (+) TAM subtype in NSCLC stratifying patient responses to immunotherapy. NSCLC patients with high TREM2+ TAM infiltration exhibited advanced tumor progression, inferior prognosis and unique NSCLC molecular characteristics, especially mutations of EGFR. TREM2+ TAMs were induced in TME, but not existed in peripheral blood. TREM2+ TAMs were enriched with multiple anti-inflammatory cytokines, exhibiting a M2-like immunosuppressive phenotype, and potentiate T cell dysfunction including impaired anti-tumor activity of CD8+ T cells and enhanced differentiation towards FOXP3+ Tregs, thus facilitating immune evasion of NSCLC. Response rates to PD-1-based ICB were higher in patients with low TREM2+ TAMs (31.58%) compared to high TREM2+ TAMs (14.29%). CONCLUSIONS Our findings implicated the immunosuppressive role of TREM2+ TAMs in NSCLC, and systematically reveal the clinical significance of TREM2+ TAMs as predictive and prognostic markers for NSCLC patients with ICB treatment.
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Lee H, Choi H. Investigating the Clinico-Molecular and Immunological Evolution of Lung Adenocarcinoma Using Pseudotime Analysis. Front Oncol 2022; 12:828505. [PMID: 35311086 PMCID: PMC8931203 DOI: 10.3389/fonc.2022.828505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction As the molecular features of lung adenocarcinoma (LUAD) have been evaluated as a cross-sectional study, the course of tumor characteristics has not been modeled. The temporal evolution of the tumor immune microenvironment (TIME), as well as the clinico-molecular features of LUAD, could provide a precise strategy for immunotherapy and surrogate biomarkers for the course of LUAD. Methods A pseudotime trajectory was constructed in patients with LUAD from the Cancer Genome Atlas and non-small cell lung cancer radiogenomics datasets. Correlation analyses were performed between clinical features and pseudotime. Genes associated with pseudotime were selected, and gene ontology analysis was performed. F-18 fluorodeoxyglucose positron emission tomography images of subjects were collected, and imaging parameters, including standardized uptake value (SUV), were obtained. Correlation analyses were performed between imaging parameters and pseudotime. Correlation analyses were performed between the enrichment scores of various immune cell types and pseudotime. In addition, correlation analyses were performed between the expression of PD-L1, tumor mutation burden, and pseudotime. Results Pseudotime trajectories of LUAD corresponded to clinical stages. Molecular profiles related to cell division and natural killer cell activity were changed along the pseudotime. The maximal SUV of LUAD tumors showed a positive correlation with pseudotime. Type 1 helper T (Th1) cells showed a positive correlation, whereas M2 macrophages showed a negative correlation with pseudotime. PD-L1 expression showed a negative correlation, whereas tumor mutation burden showed a positive correlation with pseudotime. Conclusion The estimated pseudotime associated with the stage suggested that it could reflect the clinico-molecular evolution of LUAD. Specific immune cell types in the TIME as well as cell division and glucose metabolism were dynamically changed according to the progression of the pseudotime. As a molecular progression of LUAD, different cellular targets should be considered for immunotherapy.
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Affiliation(s)
- Hyunjong Lee
- Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, South Korea
- *Correspondence: Hongyoon Choi,
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Ma X, Guo Z, Wei X, Zhao G, Han D, Zhang T, Chen X, Cao F, Dong J, Zhao L, Yuan Z, Wang P, Pang Q, Yan C, Zhang W. Spatial Distribution and Predictive Significance of Dendritic Cells and Macrophages in Esophageal Cancer Treated With Combined Chemoradiotherapy and PD-1 Blockade. Front Immunol 2022; 12:786429. [PMID: 35046943 PMCID: PMC8761740 DOI: 10.3389/fimmu.2021.786429] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 01/10/2023] Open
Abstract
Background The first clinical study (NCT03671265) of first-line chemoradiotherapy combined with PD-1 blockade showed promising treatment outcomes in locally advanced esophageal squamous cell carcinoma (ESCC). However, partial patients did not respond to the combination treatment. The roles of dendritic cells (DCs) and macrophages in this combination treatment remain poorly understood. Methods We performed multiplexed immunofluorescence method to identify CD11c+ DCs, CD68+ macrophages, and their PD-L1- or PD-L1+ subpopulations in paired tumor biopsies (n = 36) collected at baseline and during the combination treatment (after radiation, 40 Gy) from the phase Ib trial (NCT03671265). We applied whole exome sequencing in the baseline tumor biopsies (n = 14) to estimate tumor mutation burden (TMB). We dynamically investigated the spatial distribution of DCs and macrophages under chemoradiotherapy combined with PD-1 blockade, and evaluated the association between their spatial distribution and combination outcome, and TMB. Results The results showed that high percentages of PD-L1- DCs and macrophages in the baseline tumor compartment, but not in the stromal compartment, predicted improved OS and PFS. Chemoradiotherapy combined with PD-1 blockade promoted DCs and macrophages to migrate closer to tumor cells. During combination treatment, PD-L1- tumor cells were nearest to PD-L1- DCs and macrophages, while PD-L1+ tumor cells were next to PD-L1+ DCs and macrophages. High TMB was closely associated with a shorter distance from tumor cells to DCs and macrophages. Shorter distance between PD-L1+ tumor cells and PD-L1+ DCs or PD-L1- macrophages during the combination was correlated with better OS. Shorter distance between PD-L1- tumor cells and PD-L1- macrophages during combination was associated with both longer OS and PFS. Conclusions PD-L1- or PD-L1+ DCs and macrophages exhibit distinct spatial distribution in ESCC. The close distance between tumor cells and these antigen-presenting cells (APCs) is critical to the clinical outcome in chemoradiotherapy combined with PD-1 blockade in ESCC patients. Our results highlight the predictive potential of spatial patterns of APCs in chemoradiotherapy combined with immunotherapy and reveal the underlying mechanism of APCs participating in chemoradiotherapy-induced antitumor immune response in ESCC.
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Affiliation(s)
- Xiaoxue Ma
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhoubo Guo
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiaoying Wei
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Gang Zhao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Dong Han
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Tian Zhang
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xi Chen
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Fuliang Cao
- Department of Endoscopy Diagnosis and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jie Dong
- Department of Nutrition Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lujun Zhao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhiyong Yuan
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ping Wang
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Qingsong Pang
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Cihui Yan
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wencheng Zhang
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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Boyer T, Blaye C, Larmonier N, Domblides C. Influence of the Metabolism on Myeloid Cell Functions in Cancers: Clinical Perspectives. Cells 2022; 11:cells11030554. [PMID: 35159363 PMCID: PMC8834417 DOI: 10.3390/cells11030554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
Tumor metabolism plays a crucial role in sustaining tumorigenesis. There have been increasing reports regarding the role of tumor metabolism in the control of immune cell functions, generating a potent immunosuppressive contexture that can lead to immune escape. The metabolic reprogramming of tumor cells and the immune escape are two major hallmarks of cancer, with several instances of crosstalk between them. In this paper, we review the effects of tumor metabolism on immune cells, focusing on myeloid cells due to their important role in tumorigenesis and immunosuppression from the early stages of the disease. We also discuss ways to target this specific crosstalk in cancer patients.
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Affiliation(s)
- Thomas Boyer
- CNRS UMR5164, ImmunoConcEpT, Site de Carreire, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (T.B.); (C.B.); (N.L.)
- Department of Life and Medical Sciences, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Céline Blaye
- CNRS UMR5164, ImmunoConcEpT, Site de Carreire, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (T.B.); (C.B.); (N.L.)
- Department of Life and Medical Sciences, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, 229 cours de l’Argonne, 33076 Bordeaux, France
| | - Nicolas Larmonier
- CNRS UMR5164, ImmunoConcEpT, Site de Carreire, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (T.B.); (C.B.); (N.L.)
- Department of Life and Medical Sciences, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Charlotte Domblides
- CNRS UMR5164, ImmunoConcEpT, Site de Carreire, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (T.B.); (C.B.); (N.L.)
- Department of Medical Oncology, Bergonié Institute, 229 cours de l’Argonne, 33076 Bordeaux, France
- Department of Medical Oncology, Hôpital Saint-André, 1 rue Jean Burguet, University Hospital Bordeaux, 33076 Bordeaux, France
- Correspondence:
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Chen W, Guo Z, Wu J, Lin G, Chen S, Lin Q, Yang J, Xu Y, Zeng Y. Identification of a ZC3H12D-regulated competing endogenous RNA network for prognosis of lung adenocarcinoma at single-cell level. BMC Cancer 2022; 22:115. [PMID: 35090416 PMCID: PMC8796579 DOI: 10.1186/s12885-021-08992-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background To identify hub genes from the competing endogenous RNA (ceRNA) network of lung adenocarcinoma (LUAD) and to explore their potential functions on prognosis of patients from a single-cell perspective. Methods We performed RNA-sequencing of LUAD to construct ceRNA regulatory network, integrating with public databases to identify the vital pathways related to patients’ prognosis and to reveal the expression level of hub genes under different conditions, the functional enrichment of co-expressed genes and their potential immune-related mechanisms. Results ZC3H12D-hsa-miR-4443-ENST00000630242 axis was found to be related with LUAD. Lower ZC3H12D expression was significantly associated with shorter overall survival (OS) of patients (HR = 2.007, P < 0.05), and its expression was higher in early-stage patients, including T1 (P < 0.05) and N0 (P < 0.05). Additionally, ZC3H12D expression was higher in immune cells displayed by single-cell RNA-sequencing data, especially in Treg cells of lung cancer and CD8 T cells, B cells and CD4 T cells of LUAD. The functional enrichment analysis showed that the co-expressed genes mainly played a role in lymphocyte activation and cytokine-cytokine receptor interaction. In addition, ZC3H12D was associated with multiple immune cells and immune molecules, including immune checkpoints CTLA4, CD96 and TIGIT. Conclusion ZC3H12D-hsa-miR-4443-ENST00000630242 ceRNA network was identified in LUAD. ZC3H12D could affect prognosis of patients by regulating mRNA, miRNA, lncRNA, immune cells and immune molecules. Therefore, it may serve as a vital predictive marker and could be regarded as a potential therapeutic target for LUAD in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08992-1.
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Evolution and Targeting of Myeloid Suppressor Cells in Cancer: A Translational Perspective. Cancers (Basel) 2022; 14:cancers14030510. [PMID: 35158779 PMCID: PMC8833347 DOI: 10.3390/cancers14030510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Immunotherapy is achieving impressive results in the treatment of several cancers. While the main strategies aim to re-invigorate the specific lymphocyte anti-tumor response, many studies underline that altered myeloid cell frequency and functions can dramatically interfere with the responsiveness to cancer therapies. Therefore, many novel strategies targeting TAMs and MDSCs in combination with classical treatments are under continuous evolution at both pre-clinical and clinical levels, showing encouraging results. Herein, we depict a comprehensive overview of myeloid cell generation and function in a cancer setting, and the most relevant strategies for their targeting that are currently in clinical use or under pre-clinical development. Abstract In recent years, the immune system has emerged as a critical regulator of tumor development, progression and dissemination. Advanced therapeutic approaches targeting immune cells are currently under clinical use and improvement for the treatment of patients affected by advanced malignancies. Among these, anti-PD1/PD-L1 and anti-CTLA4 immune checkpoint inhibitors (ICIs) are the most effective immunotherapeutic drugs at present. In spite of these advances, great variability in responses to therapy exists among patients, probably due to the heterogeneity of both cancer cells and immune responses, which manifest in diverse forms in the tumor microenvironment (TME). The variability of the immune profile within TME and its prognostic significance largely depend on the frequency of the infiltrating myeloid cells, which often represent the predominant population, characterized by high phenotypic heterogeneity. The generation of heterogeneous myeloid populations endowed with tumor-promoting activities is typically promoted by growing tumors, indicating the sequential levels of myeloid reprogramming as possible antitumor targets. This work reviews the current knowledge on the events governing protumoral myelopoiesis, analyzing the mechanisms that drive the expansion of major myeloid subsets, as well as their functional properties, and highlighting recent translational strategies for clinical developments.
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Zhang J, Song C, Tian Y, Yang X. Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment. Front Immunol 2022; 12:802080. [PMID: 35126365 PMCID: PMC8807562 DOI: 10.3389/fimmu.2021.802080] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
The lung tumor microenvironment, which is composed of heterogeneous cell populations, plays an important role in the progression of lung cancer and is closely related to therapeutic efficacy. Increasing evidence has shown that stromal components play a key role in regulating tumor invasion, metastasis and drug resistance. Therefore, a better understanding of stromal components in the tumor microenvironment is helpful for the diagnosis and treatment of lung cancer. Rapid advances in technology have brought our understanding of disease into the genetic era, and single-cell RNA sequencing has enabled us to describe gene expression profiles with unprecedented resolution, enabling quantitative analysis of gene expression at the single-cell level to reveal the correlations among heterogeneity, signaling pathways, drug resistance and microenvironment molding in lung cancer, which is important for the treatment of this disease. In this paper, several common single-cell RNA sequencing methods and their advantages and disadvantages are briefly introduced to provide a reference for selection of suitable methods. Furthermore, we review the latest progress of single-cell RNA sequencing in the study of stromal cells in the lung tumor microenvironment.
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Rams M, Conrad TOF. Dictionary learning allows model-free pseudotime estimation of transcriptomic data. BMC Genomics 2022; 23:56. [PMID: 35033004 PMCID: PMC8760643 DOI: 10.1186/s12864-021-08276-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Pseudotime estimation from dynamic single-cell transcriptomic data enables characterisation and understanding of the underlying processes, for example developmental processes. Various pseudotime estimation methods have been proposed during the last years. Typically, these methods start with a dimension reduction step because the low-dimensional representation is usually easier to analyse. Approaches such as PCA, ICA or t-SNE belong to the most widely used methods for dimension reduction in pseudotime estimation methods. However, these methods usually make assumptions on the derived dimensions, which can result in important dataset properties being missed. In this paper, we suggest a new dictionary learning based approach, dynDLT, for dimension reduction and pseudotime estimation of dynamic transcriptomic data. Dictionary learning is a matrix factorisation approach that does not restrict the dependence of the derived dimensions. To evaluate the performance, we conduct a large simulation study and analyse 8 real-world datasets. Results The simulation studies reveal that firstly, dynDLT preserves the simulated patterns in low-dimension and the pseudotimes can be derived from the low-dimensional representation. Secondly, the results show that dynDLT is suitable for the detection of genes exhibiting the simulated dynamic patterns, thereby facilitating the interpretation of the compressed representation and thus the dynamic processes. For the real-world data analysis, we select datasets with samples that are taken at different time points throughout an experiment. The pseudotimes found by dynDLT have high correlations with the experimental times. We compare the results to other approaches used in pseudotime estimation, or those that are method-wise closely connected to dictionary learning: ICA, NMF, PCA, t-SNE, and UMAP. DynDLT has the best overall performance for the simulated and real-world datasets. Conclusions We introduce dynDLT, a method that is suitable for pseudotime estimation. Its main advantages are: (1) It presents a model-free approach, meaning that it does not restrict the dependence of the derived dimensions; (2) Genes that are relevant in the detected dynamic processes can be identified from the dictionary matrix; (3) By a restriction of the dictionary entries to positive values, the dictionary atoms are highly interpretable. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08276-9).
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Affiliation(s)
- Mona Rams
- Freie Universitaet Berlin, Arnimallee 6, Berlin, 14195, Germany.
| | - Tim O F Conrad
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, Takustraße 7, Berlin, 14195, Germany
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